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| Status |
Public on Dec 30, 2021 |
| Title |
HepG2 WGBS rep1 |
| Sample type |
SRA |
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| Source name |
HepG2 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
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| Growth protocol |
HepG2 were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from HepG2 cells was extracted with the Qiagen DNeasy Blood and Tissue Kit following the manufacturer’s instructions. Extracted DNA was converted with EZ DNA Methylation-Gold Kit from Zymo. The extracted DNA was followed by bisulfite conversion using the EZ DNA Methylation-Gold Kit from Zymo according to manufacturer’s instructions.
Illumina Paired End (125 PE) for WGBS
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Re-analysis of:
GSM2308630
Raw files:
ENCFF406GDR ENCFF508BUS
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR881XOU/
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| Data processing |
Fastq files were downloaded from ENCODE portal (https://www.encodeproject.org/) for 2 replicates
Reads were trimmed(3-4bp from ends) using trim galore(version 0.3.7), powered by cutadapt to trim adaptor sequences for QC purpose
WGBS reads were processed with Bismark(bismark-0.11.1) pipeline using Bowtie2(bowtie-2-2.1.0) aligner
Deduplication and PCR duplicates removal was performed using deduplicate_bismark program
Methylation extraction from deduplicated bam files, in CpG context, was performed using bismark_methylation_extractor program
Genome_build: hg19
Supplementary_files_format_and_content: .bedGraph - [Chromosome number, start position, stop position, dataValue], .cov - [Chromosome number, start position, stop position, methylation percent, methylated reads, unmethylated reads]
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| Submission date |
Sep 26, 2017 |
| Last update date |
Dec 30, 2021 |
| Contact name |
Eric M Mendenhall |
| E-mail(s) |
emendenhall@hudsonalpha.org
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| Organization name |
HudsonAlpha Institute
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| Lab |
Mendenhall Lab
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| Street address |
601 Genome Way Northwest
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| City |
Huntsville |
| State/province |
AL |
| ZIP/Postal code |
35806 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE104245 |
Whole genome methylation profiling in HepG2 cells using WGBS (Whole Genome Bisulfite Sequencing) |
| GSE104248 |
Towards an integrative map of a single cell type's transcription factor landscape |
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| Relations |
| BioSample |
SAMN07702228 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2793708_SL83768_CpG_context_deduplicated.bedGraph.gz |
340.4 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM2793708_SL83768_CpG_context_deduplicated.bismark.cov.gz |
357.7 Mb |
(ftp)(http) |
COV |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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